Trimmomatic can't find the adapter files

Question

[john]

Trimmomatic can't seem to find my adapter files, and I've tried a lot of different pathways but nothing works. Any help is appreciated, thanks.

Here's my code:

for file in ../../fqgz_trim_single/*R1_001.fastq.gz
do
  trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:100 CROP:100
done

The adapters are located in the same folder as the raw reads. If I change the pathway to ../../TruSeq3-SE.fa:2:30:10 that doesn't work neither.

Thanks

Answer 1

[Pierre Lindenbaum]

The syntax is

java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Here, trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEA... you don't provide any output file.

[john]

Oh I see. But how do I then provide the output such that I get a new file for every file that is being trimmed?

[GenoMax]

Use a loop to loop through your files. See: How to loop to use trimmomatic for multiple fastq files?

[john]

Thank you!